Devices, systems, and methods for virtual staining
The disclosure herein provides methods, systems, and devices for virtually staining biological tissue for enhanced visualization without use of an actual dye or tag by detecting how each pixel of an unstained tissue image changes in waveform after staining with a certain dye(s) and/or tag(s) or other transformation under a certain electromagnetic radiation source, developing a virtual staining transform based on such detection, and applying such virtual staining transform to an unstained biological tissue to virtually stain the tissue.
1. A system for virtually staining a tissue sample, the system comprising:
at least one hardware processor; and
at least one non-transitory memory storing instructions which, when executed by the at least one hardware processor, cause the system to:
access an electronic medical image of the tissue sample, the electronic medical image of the tissue sample comprising a plurality of pixels generated based on electromagnetic radiation detected by a detector, wherein the plurality of pixels comprises a first pixel and a second pixel;
determine that a first waveform signature associated with the first pixel of the plurality of pixels is based on a combination of a first plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the first pixel;
determine the first plurality of waveform signatures;
apply transformation data to the first plurality of waveform signatures in order to obtain a first plurality of outputs;
determine a first single output pixel by volume averaging the first plurality of outputs;
generate a virtually stained first input image of the tissue sample, wherein the virtually stained first input image comprises at least a first single output pixel;
determine that a second waveform signature associated with the second pixel of the plurality of pixels is based on a combination of a second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel;
determine the second plurality of waveform signatures;
apply transformation data to the second plurality of waveform signatures in order to obtain a second plurality of outputs;
determine a second single output pixel by volume averaging the second plurality of outputs;
generate a virtually stained second input image of the tissue sample, wherein the virtually stained second input image comprises at least a second single output pixel;
generate a combined virtually stained image of the tissue sample comprising the virtually stained first input image and the virtually stained second input image; and
display the combined virtually stained image of the tissue sample, wherein the combined virtually stained image is substantially identical to an image of the tissue sample when the tissue sample is treated with an actual stain that corresponds to a virtual stain defined by a virtual staining transform.
2. The system for virtually staining a tissue sample of claim 1 , wherein the detector is a multi-spectrum detector.
3. The system for virtually staining a tissue sample of claim 1 , wherein the tissue sample is in vitro.
4. The system for virtually staining a tissue sample of claim 1 , wherein the determining based on the combination of the first plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the first pixel and the determining based on the combination of the second plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the second pixel is based at least in part on a first identified vector signature associated with the first pixel of the plurality of pixels and a second identified vector signature associated with the second pixel of the plurality of pixels.
5. The system for virtually staining a tissue sample of claim 1 , wherein the tissue sample is a three-dimensional tissue sample.
6. The system for virtually staining a tissue sample of claim 5 , wherein the detector is configured to change a focal depth to obtain two-dimensional electromagnetic radiation data at varying z depths of the three-dimensional tissue sample.
7. The system for virtually staining a tissue sample of claim 1 , wherein the detector is incorporated into a medical probe.
8. The system for virtually staining a tissue sample of claim 1 , wherein the actual stain is a dye configured to color certain portions of the tissue sample.
9. The system for virtually staining a tissue sample of claim 1 , wherein the actual stain is a tag.
10. The system for virtually staining a tissue sample of claim 9 , wherein the tag is at least one of an antibody, an aptamer, or a fluorescent protein.
11. A method for virtually staining a tissue sample, the method comprising:
accessing an electronic medical image of the tissue sample, the electronic medical image of the tissue sample comprising a plurality of pixels generated based on electromagnetic radiation detected by a detector, wherein the plurality of pixels comprises a first pixel and a second pixel;
determining that a first waveform signature associated with the first pixel of the plurality of pixels is based on a combination of a first plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the first pixel;
determining the first plurality of waveform signatures;
applying transformation data to the first plurality of waveform signatures in order to obtain a first plurality of outputs;
determining a first single output pixel by volume averaging the first plurality of outputs;
generating a virtually stained first input image of the tissue sample, wherein the virtually stained first input image comprises at least the first single output pixel;
determining that a second waveform signature associated with the second pixel of the plurality of pixels is based on a combination of a second plurality of waveform signatures corresponding to multiple substances in the tissue sample at a location associated with the second pixel;
determining the second plurality of waveform signatures;
applying transformation data to the second plurality of waveform signatures in order to obtain a second plurality of outputs;
determining a second single output pixel by volume averaging the second plurality of outputs;
generating a virtually stained second input image of the tissue sample, wherein the virtually stained second input image comprises at least the second single output pixel;
generating a combined virtually stained image of the tissue sample comprising the virtually stained first input image and the virtually stained second input image; and
displaying the combined virtually stained image of the tissue sample, wherein the combined virtually stained image is substantially identical to an image of the tissue sample when the tissue sample is treated with an actual stain that corresponds to a virtual stain defined by a virtual staining transform.
12. The method of claim 11 , wherein the detector is a multi-spectrum detector.
13. The method of claim 11 , wherein the tissue sample is in vitro.
14. The method of claim 11 , wherein the determining based on the combination of the first plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the first pixel and the determining based on the combination of the second plurality of waveform signatures corresponding to multiple substances in the tissue sample at the location associated with the second pixel is based at least in part on a first identified vector signature associated the first pixel of the plurality of pixels and a second identified vector signature associated with the second pixel of the plurality of pixels.
15. The method of claim 11 , wherein the tissue sample is a three-dimensional tissue sample.
16. The method of claim 15 , wherein the detector is configured to change a focal depth to obtain two-dimensional electromagnetic radiation data at varying z depths of the three-dimensional tissue sample.
17. The method of claim 11 , wherein the detector is incorporated into a medical probe.
18. The method of claim 11 , wherein the actual stain is at least one of a dye configured to color certain portions of the tissue sample.
19. The method of claim 11 , wherein the actual stain is a tag.
20. The method of claim 19 , wherein the tag is at least one of an antibody, an aptamer, or a fluorescent protein.